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bioRxiv · 10.1101/2022.07.12.499770

Evolution of the regulation of developmental gene expression in blind Mexican cavefish

Leclercq, J.·Torres-Paz, J.·Policarpo, M.·Agnes, F.·Retaux, S.
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Abstract

Changes in gene expression regulation during development are considered the main drivers of morphological evolution and diversification. Here, we analysed the embryonic transcriptomes of surface-dwelling and blind cave-adapted morphs of the species Astyanax mexicanus and their reciprocal F1 hybrids at tailbud stage. Comparing gene expression in parents and allelic expression ratios in hybrids, we found that [~]20% of the transcriptome is differentially expressed and that cis-regulatory changes are the main contributors to variations in early developmental gene expression in the two morphs. We provide a list of 108 cis-regulated genes that could contribute to cavefish developmental evolution, and further explore the regulatory mechanisms controlling the cellular and regional expression of rx3, a "master eye gene". Using quantitative embryology approaches after fluorescent in situ hybridisation, cell transplantations and interference with signalling pathways, we show that rx3 cellular levels -controlling optic cell fates-are regulated in cis and in a cell-autonomous manner, whereas the size of rx3 domain -controlling eye size-depends on non-autonomous Wnt signalling. Altogether, we reveal how distinct mechanisms and regulatory modules can regulate developmental gene expression and shape developmental evolution, with negligible contribution of coding mutations.

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Leclercq, J., Torres-Paz, J., Policarpo, M., Agnes, F., Retaux, S.. 2022-07-14. Evolution of the regulation of developmental gene expression in blind Mexican cavefish. https://doi.org/10.1101/2022.07.12.499770

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